After some testing I found out the issue and I think I solved it.
The key thing is the orth value.
If нёбо has <idx

rth value="нёбо"> and небо has <idx

rth value="не́бо">, only нёбо gets picked up.
If нёбо has <idx

rth value="нёбо"> and небо has <idx

rth value="небо"> only небо gets picked up.
If both have <idx

rth value="небо">, both get picked up and display 1/2 with the arrows.
So I think it may be safe to assume that values in orth tags are to be written without any diacritics.